Starting phenix.real_space_refine on Wed Sep 17 17:25:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6slu_10240/09_2025/6slu_10240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6slu_10240/09_2025/6slu_10240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6slu_10240/09_2025/6slu_10240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6slu_10240/09_2025/6slu_10240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6slu_10240/09_2025/6slu_10240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6slu_10240/09_2025/6slu_10240.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6508 2.51 5 N 1800 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 3.71, per 1000 atoms: 0.36 Number of scatterers: 10336 At special positions: 0 Unit cell: (114.68, 113.46, 84.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1950 8.00 N 1800 7.00 C 6508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=1.53 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.19 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 546.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 67.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.512A pdb=" N GLU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.194A pdb=" N ASN A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.596A pdb=" N LYS B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.209A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.587A pdb=" N GLN B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.524A pdb=" N ILE B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.578A pdb=" N LYS B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.955A pdb=" N MET B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.606A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.616A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.627A pdb=" N MET C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.695A pdb=" N TYR C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.624A pdb=" N GLN C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.549A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.719A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.703A pdb=" N TRP D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 220 removed outlier: 3.532A pdb=" N GLY D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.633A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 4.008A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.177A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.649A pdb=" N GLN E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 191 removed outlier: 4.189A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.970A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.730A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.546A pdb=" N MET F 66 " --> pdb=" O HIS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 119 removed outlier: 3.507A pdb=" N GLN F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 160 through 174 removed outlier: 3.554A pdb=" N TYR F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.617A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.716A pdb=" N GLN F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.568A pdb=" N VAL A 3 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 11 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.466A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.795A pdb=" N VAL D 3 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 11 " --> pdb=" O VAL D 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.587A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 577 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3210 1.34 - 1.46: 1348 1.46 - 1.57: 5864 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 10566 Sorted by residual: bond pdb=" N PRO D 38 " pdb=" CD PRO D 38 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N PRO A 34 " pdb=" CD PRO A 34 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 bond pdb=" C SER A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.335 1.388 -0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" N PRO D 34 " pdb=" CD PRO D 34 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO A 38 " pdb=" CD PRO A 38 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14194 2.64 - 5.28: 155 5.28 - 7.92: 13 7.92 - 10.56: 0 10.56 - 13.20: 4 Bond angle restraints: 14366 Sorted by residual: angle pdb=" CA ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 121.00 114.87 6.13 8.30e-01 1.45e+00 5.45e+01 angle pdb=" N GLU C 29 " pdb=" CA GLU C 29 " pdb=" C GLU C 29 " ideal model delta sigma weight residual 111.36 118.40 -7.04 1.09e+00 8.42e-01 4.18e+01 angle pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" C GLU B 29 " ideal model delta sigma weight residual 111.36 118.22 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" C ILE E 37 " pdb=" CA ILE E 37 " pdb=" CB ILE E 37 " ideal model delta sigma weight residual 114.35 107.80 6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" O ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 120.07 124.09 -4.02 7.10e-01 1.98e+00 3.21e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6209 17.92 - 35.84: 276 35.84 - 53.76: 31 53.76 - 71.68: 2 71.68 - 89.60: 4 Dihedral angle restraints: 6522 sinusoidal: 2704 harmonic: 3818 Sorted by residual: dihedral pdb=" CB CYS C 198 " pdb=" SG CYS C 198 " pdb=" SG CYS C 218 " pdb=" CB CYS C 218 " ideal model delta sinusoidal sigma weight residual -86.00 -12.93 -73.07 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS F 198 " pdb=" SG CYS F 198 " pdb=" SG CYS F 218 " pdb=" CB CYS F 218 " ideal model delta sinusoidal sigma weight residual -86.00 -117.96 31.96 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" C PHE E 32 " pdb=" N PHE E 32 " pdb=" CA PHE E 32 " pdb=" CB PHE E 32 " ideal model delta harmonic sigma weight residual -122.60 -130.68 8.08 0 2.50e+00 1.60e-01 1.04e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1223 0.044 - 0.088: 278 0.088 - 0.132: 81 0.132 - 0.177: 16 0.177 - 0.221: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LYS C 30 " pdb=" N LYS C 30 " pdb=" C LYS C 30 " pdb=" CB LYS C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL F 27 " pdb=" N VAL F 27 " pdb=" C VAL F 27 " pdb=" CB VAL F 27 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1601 not shown) Planarity restraints: 1882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 37 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO E 38 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 35 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLU F 35 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU F 35 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL F 36 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 19 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C THR E 19 " 0.027 2.00e-02 2.50e+03 pdb=" O THR E 19 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU E 20 " -0.009 2.00e-02 2.50e+03 ... (remaining 1879 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 3 2.14 - 2.83: 3257 2.83 - 3.52: 14581 3.52 - 4.21: 22149 4.21 - 4.90: 38246 Nonbonded interactions: 78236 Sorted by model distance: nonbonded pdb=" O THR D 58 " pdb=" OE2 GLU E 35 " model vdw 1.454 3.040 nonbonded pdb=" O PRO F 17 " pdb=" OD1 ASN F 21 " model vdw 2.029 3.040 nonbonded pdb=" OE1 GLU C 71 " pdb=" OG1 THR D 210 " model vdw 2.099 3.040 nonbonded pdb=" NZ LYS C 30 " pdb=" OE2 GLU C 35 " model vdw 2.202 3.120 nonbonded pdb=" O PRO F 17 " pdb=" CG ASN F 21 " model vdw 2.202 3.270 ... (remaining 78231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.505 10572 Z= 0.358 Angle : 0.753 44.137 14378 Z= 0.462 Chirality : 0.044 0.221 1604 Planarity : 0.004 0.070 1882 Dihedral : 9.227 89.598 4028 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.21), residues: 1310 helix: -0.14 (0.17), residues: 814 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.004 0.001 TYR E 130 PHE 0.012 0.001 PHE E 32 TRP 0.003 0.001 TRP E 184 HIS 0.001 0.000 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00352 (10566) covalent geometry : angle 0.63868 (14366) SS BOND : bond 0.21557 ( 6) SS BOND : angle 13.84675 ( 12) hydrogen bonds : bond 0.13364 ( 577) hydrogen bonds : angle 4.66297 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 639 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.9257 (tt0) cc_final: 0.8519 (tm-30) REVERT: A 68 MET cc_start: 0.9330 (mtp) cc_final: 0.8284 (mtt) REVERT: A 71 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 115 ILE cc_start: 0.9581 (mm) cc_final: 0.9374 (mm) REVERT: A 117 TRP cc_start: 0.6047 (m-10) cc_final: 0.5720 (m-10) REVERT: A 129 ILE cc_start: 0.9089 (mt) cc_final: 0.8530 (tt) REVERT: A 141 ILE cc_start: 0.9566 (mm) cc_final: 0.9324 (tp) REVERT: A 202 LEU cc_start: 0.9062 (mt) cc_final: 0.8815 (mm) REVERT: B 26 VAL cc_start: 0.9286 (p) cc_final: 0.9070 (m) REVERT: B 38 PRO cc_start: 0.9363 (Cg_exo) cc_final: 0.9057 (Cg_endo) REVERT: B 76 GLU cc_start: 0.9320 (tt0) cc_final: 0.9021 (tp30) REVERT: B 81 ASP cc_start: 0.9302 (t0) cc_final: 0.8508 (t0) REVERT: B 100 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8626 (tpm170) REVERT: B 113 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9279 (mt-10) REVERT: B 114 GLN cc_start: 0.9731 (pt0) cc_final: 0.9073 (pt0) REVERT: B 128 GLU cc_start: 0.9465 (mp0) cc_final: 0.8944 (pp20) REVERT: B 129 ILE cc_start: 0.9656 (mm) cc_final: 0.9208 (tp) REVERT: B 141 ILE cc_start: 0.8869 (mt) cc_final: 0.8299 (mt) REVERT: B 144 MET cc_start: 0.8668 (tmm) cc_final: 0.8459 (ppp) REVERT: B 190 LEU cc_start: 0.9061 (mt) cc_final: 0.8771 (mt) REVERT: C 35 GLU cc_start: 0.8808 (pt0) cc_final: 0.8039 (tm-30) REVERT: C 53 ASN cc_start: 0.8562 (m-40) cc_final: 0.8257 (t0) REVERT: C 68 MET cc_start: 0.9550 (mtp) cc_final: 0.8817 (mtt) REVERT: C 75 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8194 (pp20) REVERT: C 76 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8756 (mm-30) REVERT: C 98 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8736 (tm-30) REVERT: C 129 ILE cc_start: 0.9593 (mt) cc_final: 0.9386 (pt) REVERT: C 159 GLU cc_start: 0.8929 (mp0) cc_final: 0.8344 (pt0) REVERT: C 167 ARG cc_start: 0.8883 (ttt180) cc_final: 0.8622 (ptp-170) REVERT: D 16 SER cc_start: 0.9226 (t) cc_final: 0.8934 (p) REVERT: D 23 TRP cc_start: 0.9287 (t-100) cc_final: 0.8785 (t-100) REVERT: D 32 PHE cc_start: 0.7450 (m-80) cc_final: 0.7066 (m-80) REVERT: D 37 ILE cc_start: 0.9256 (mt) cc_final: 0.9046 (mt) REVERT: D 48 THR cc_start: 0.9592 (p) cc_final: 0.9382 (t) REVERT: D 50 GLN cc_start: 0.9237 (tt0) cc_final: 0.8852 (tm-30) REVERT: D 51 ASP cc_start: 0.9221 (m-30) cc_final: 0.8784 (m-30) REVERT: D 55 MET cc_start: 0.9222 (ttm) cc_final: 0.8982 (ttm) REVERT: D 68 MET cc_start: 0.9208 (mtp) cc_final: 0.8929 (mtp) REVERT: D 71 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8863 (mt-10) REVERT: D 95 GLN cc_start: 0.6789 (tp40) cc_final: 0.6530 (pt0) REVERT: D 128 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 129 ILE cc_start: 0.9091 (mt) cc_final: 0.8646 (tt) REVERT: D 138 LEU cc_start: 0.9493 (mt) cc_final: 0.9252 (tp) REVERT: D 152 ASP cc_start: 0.8092 (m-30) cc_final: 0.7870 (p0) REVERT: D 170 LYS cc_start: 0.9281 (tttt) cc_final: 0.9074 (tptt) REVERT: D 181 VAL cc_start: 0.8561 (p) cc_final: 0.8053 (p) REVERT: D 215 MET cc_start: 0.9067 (mtm) cc_final: 0.8466 (mtm) REVERT: E 28 GLU cc_start: 0.8953 (tt0) cc_final: 0.8546 (pt0) REVERT: E 95 GLN cc_start: 0.6651 (mm110) cc_final: 0.6361 (pt0) REVERT: E 100 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8296 (tpp-160) REVERT: E 128 GLU cc_start: 0.9296 (mp0) cc_final: 0.8781 (pp20) REVERT: E 141 ILE cc_start: 0.8994 (mt) cc_final: 0.8447 (mt) REVERT: E 144 MET cc_start: 0.8239 (ppp) cc_final: 0.7839 (ppp) REVERT: E 161 PHE cc_start: 0.8011 (t80) cc_final: 0.7745 (t80) REVERT: F 52 LEU cc_start: 0.9832 (mp) cc_final: 0.9495 (mp) REVERT: F 68 MET cc_start: 0.9612 (mtp) cc_final: 0.9051 (mtt) REVERT: F 79 GLU cc_start: 0.9572 (tt0) cc_final: 0.9202 (tp30) REVERT: F 98 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8638 (tm-30) REVERT: F 129 ILE cc_start: 0.9596 (mt) cc_final: 0.9276 (pt) REVERT: F 141 ILE cc_start: 0.9231 (mt) cc_final: 0.9017 (mt) REVERT: F 142 VAL cc_start: 0.9263 (m) cc_final: 0.9014 (p) REVERT: F 158 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8275 (mmmt) REVERT: F 159 GLU cc_start: 0.9066 (mp0) cc_final: 0.8569 (pt0) REVERT: F 164 TYR cc_start: 0.8638 (t80) cc_final: 0.7050 (t80) REVERT: F 185 MET cc_start: 0.8997 (ptp) cc_final: 0.8775 (ptp) REVERT: F 191 VAL cc_start: 0.8860 (p) cc_final: 0.8093 (p) REVERT: F 216 THR cc_start: 0.8760 (p) cc_final: 0.8251 (p) outliers start: 2 outliers final: 1 residues processed: 639 average time/residue: 0.1419 time to fit residues: 117.7439 Evaluate side-chains 392 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 7 GLN A 9 GLN A 87 HIS A 95 GLN B 21 ASN B 53 ASN B 95 GLN C 4 GLN C 5 ASN C 67 GLN C 139 ASN C 192 GLN D 4 GLN D 9 GLN D 87 HIS D 112 GLN D 183 ASN E 13 GLN E 50 GLN E 67 GLN E 95 GLN F 4 GLN F 139 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068431 restraints weight = 81282.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072419 restraints weight = 41325.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075341 restraints weight = 26759.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077497 restraints weight = 19399.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079087 restraints weight = 15137.783| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10572 Z= 0.142 Angle : 0.637 8.199 14378 Z= 0.324 Chirality : 0.044 0.161 1604 Planarity : 0.005 0.048 1882 Dihedral : 3.412 16.832 1404 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.22), residues: 1310 helix: 0.44 (0.17), residues: 822 sheet: None (None), residues: 0 loop : -0.94 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 173 TYR 0.015 0.002 TYR E 145 PHE 0.023 0.002 PHE D 161 TRP 0.021 0.002 TRP A 80 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00320 (10566) covalent geometry : angle 0.63470 (14366) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.89275 ( 12) hydrogen bonds : bond 0.03979 ( 577) hydrogen bonds : angle 3.79984 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 506 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8590 (tt0) cc_final: 0.8291 (pp20) REVERT: A 50 GLN cc_start: 0.9266 (tt0) cc_final: 0.8607 (tm-30) REVERT: A 51 ASP cc_start: 0.9331 (m-30) cc_final: 0.8579 (m-30) REVERT: A 68 MET cc_start: 0.9437 (mtp) cc_final: 0.8862 (mtt) REVERT: A 82 ARG cc_start: 0.9383 (ptm-80) cc_final: 0.9165 (ttp80) REVERT: A 100 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.8718 (ptm-80) REVERT: A 141 ILE cc_start: 0.9617 (mm) cc_final: 0.9364 (tp) REVERT: A 144 MET cc_start: 0.9021 (tpp) cc_final: 0.8369 (tpp) REVERT: A 167 ARG cc_start: 0.9347 (mtm-85) cc_final: 0.8904 (ptt-90) REVERT: A 215 MET cc_start: 0.8508 (ptm) cc_final: 0.7878 (ptm) REVERT: B 10 MET cc_start: 0.5991 (tmm) cc_final: 0.5611 (tmm) REVERT: B 38 PRO cc_start: 0.9446 (Cg_exo) cc_final: 0.9231 (Cg_endo) REVERT: B 55 MET cc_start: 0.9538 (ttm) cc_final: 0.9095 (tpp) REVERT: B 100 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8591 (tpm170) REVERT: B 128 GLU cc_start: 0.9408 (mp0) cc_final: 0.8841 (pp20) REVERT: B 129 ILE cc_start: 0.9637 (mm) cc_final: 0.8988 (tp) REVERT: B 141 ILE cc_start: 0.8656 (mt) cc_final: 0.8398 (mt) REVERT: B 190 LEU cc_start: 0.8848 (mt) cc_final: 0.8348 (mt) REVERT: C 9 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8036 (pm20) REVERT: C 35 GLU cc_start: 0.8982 (pt0) cc_final: 0.8342 (tm-30) REVERT: C 53 ASN cc_start: 0.8600 (m-40) cc_final: 0.8392 (t0) REVERT: C 66 MET cc_start: 0.8834 (mpp) cc_final: 0.8541 (mpp) REVERT: C 68 MET cc_start: 0.9456 (mtp) cc_final: 0.8665 (mtt) REVERT: C 96 MET cc_start: 0.2764 (mpp) cc_final: 0.1942 (mpp) REVERT: C 98 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8736 (tm-30) REVERT: C 104 ILE cc_start: 0.9074 (tt) cc_final: 0.8643 (mt) REVERT: C 114 GLN cc_start: 0.8810 (mp-120) cc_final: 0.8111 (mp10) REVERT: C 159 GLU cc_start: 0.8785 (mp0) cc_final: 0.8511 (pt0) REVERT: C 167 ARG cc_start: 0.8981 (ttt180) cc_final: 0.8699 (ptp90) REVERT: C 186 THR cc_start: 0.9050 (p) cc_final: 0.8779 (p) REVERT: C 215 MET cc_start: 0.8920 (ptp) cc_final: 0.8703 (ppp) REVERT: C 216 THR cc_start: 0.8654 (p) cc_final: 0.7947 (p) REVERT: D 16 SER cc_start: 0.9297 (t) cc_final: 0.8932 (p) REVERT: D 23 TRP cc_start: 0.9631 (t-100) cc_final: 0.9333 (t-100) REVERT: D 50 GLN cc_start: 0.9341 (tt0) cc_final: 0.8885 (tm-30) REVERT: D 51 ASP cc_start: 0.8755 (m-30) cc_final: 0.8124 (m-30) REVERT: D 55 MET cc_start: 0.9404 (ttm) cc_final: 0.9057 (ttp) REVERT: D 67 GLN cc_start: 0.9512 (mm-40) cc_final: 0.9273 (mt0) REVERT: D 111 LEU cc_start: 0.9509 (tp) cc_final: 0.9263 (tp) REVERT: D 129 ILE cc_start: 0.9136 (mt) cc_final: 0.8713 (tt) REVERT: D 132 ARG cc_start: 0.9524 (mtp-110) cc_final: 0.9159 (ttp-110) REVERT: D 215 MET cc_start: 0.8873 (mtm) cc_final: 0.8388 (mtm) REVERT: E 28 GLU cc_start: 0.8870 (tt0) cc_final: 0.8471 (pt0) REVERT: E 30 LYS cc_start: 0.8922 (tppt) cc_final: 0.8333 (tptp) REVERT: E 55 MET cc_start: 0.9642 (ttm) cc_final: 0.9260 (tpp) REVERT: E 68 MET cc_start: 0.8873 (mtp) cc_final: 0.8673 (mtp) REVERT: E 100 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8722 (tpp-160) REVERT: E 128 GLU cc_start: 0.9209 (mp0) cc_final: 0.8755 (tm-30) REVERT: E 129 ILE cc_start: 0.9488 (mm) cc_final: 0.8734 (mm) REVERT: E 131 LYS cc_start: 0.9583 (tttt) cc_final: 0.9370 (tttt) REVERT: E 132 ARG cc_start: 0.9322 (mtm110) cc_final: 0.9024 (mtm110) REVERT: E 141 ILE cc_start: 0.8766 (mt) cc_final: 0.8371 (mt) REVERT: E 190 LEU cc_start: 0.8923 (mt) cc_final: 0.8677 (mt) REVERT: F 13 GLN cc_start: 0.9372 (tp40) cc_final: 0.9163 (tp-100) REVERT: F 38 PRO cc_start: 0.9474 (Cg_exo) cc_final: 0.9259 (Cg_endo) REVERT: F 39 MET cc_start: 0.9196 (tpp) cc_final: 0.8980 (tpp) REVERT: F 68 MET cc_start: 0.9629 (mtp) cc_final: 0.8894 (mtt) REVERT: F 71 GLU cc_start: 0.9219 (tm-30) cc_final: 0.9010 (tm-30) REVERT: F 75 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 79 GLU cc_start: 0.9581 (tt0) cc_final: 0.9177 (tp30) REVERT: F 111 LEU cc_start: 0.9087 (tp) cc_final: 0.8263 (mp) REVERT: F 117 TRP cc_start: 0.8370 (m-10) cc_final: 0.7745 (m-90) REVERT: F 129 ILE cc_start: 0.9646 (mt) cc_final: 0.9186 (mm) REVERT: F 132 ARG cc_start: 0.9453 (mtp-110) cc_final: 0.9063 (ptm-80) REVERT: F 141 ILE cc_start: 0.9553 (mt) cc_final: 0.9231 (mm) REVERT: F 142 VAL cc_start: 0.9414 (m) cc_final: 0.9150 (p) REVERT: F 158 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8224 (mmmt) REVERT: F 164 TYR cc_start: 0.8169 (t80) cc_final: 0.7169 (t80) REVERT: F 168 PHE cc_start: 0.9462 (t80) cc_final: 0.9210 (t80) REVERT: F 179 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8967 (tp-100) REVERT: F 185 MET cc_start: 0.8869 (ptp) cc_final: 0.8659 (ptp) REVERT: F 190 LEU cc_start: 0.8888 (mt) cc_final: 0.8406 (mt) outliers start: 1 outliers final: 0 residues processed: 507 average time/residue: 0.1388 time to fit residues: 91.8212 Evaluate side-chains 379 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN D 95 GLN D 112 GLN E 13 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.064983 restraints weight = 71417.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068466 restraints weight = 39116.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071037 restraints weight = 26258.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072882 restraints weight = 19605.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074300 restraints weight = 15723.182| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10572 Z= 0.159 Angle : 0.658 8.261 14378 Z= 0.339 Chirality : 0.045 0.174 1604 Planarity : 0.005 0.049 1882 Dihedral : 3.761 15.586 1404 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1310 helix: 0.52 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.74 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 167 TYR 0.016 0.001 TYR D 169 PHE 0.020 0.002 PHE B 40 TRP 0.024 0.002 TRP C 23 HIS 0.004 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00355 (10566) covalent geometry : angle 0.65708 (14366) SS BOND : bond 0.00109 ( 6) SS BOND : angle 1.09598 ( 12) hydrogen bonds : bond 0.03914 ( 577) hydrogen bonds : angle 3.86879 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5409 (tpt) cc_final: 0.5192 (mmm) REVERT: A 68 MET cc_start: 0.9463 (mtp) cc_final: 0.9081 (mtt) REVERT: A 82 ARG cc_start: 0.9372 (ptm-80) cc_final: 0.9143 (ttp80) REVERT: A 100 ARG cc_start: 0.9004 (ptm-80) cc_final: 0.8703 (ptm-80) REVERT: A 129 ILE cc_start: 0.9004 (mt) cc_final: 0.8788 (mt) REVERT: A 141 ILE cc_start: 0.9653 (mm) cc_final: 0.9389 (tp) REVERT: A 144 MET cc_start: 0.8924 (tpp) cc_final: 0.8273 (tpp) REVERT: A 167 ARG cc_start: 0.9257 (mtm-85) cc_final: 0.8867 (ptt-90) REVERT: A 215 MET cc_start: 0.8521 (ptm) cc_final: 0.7985 (ptm) REVERT: B 10 MET cc_start: 0.5858 (tmm) cc_final: 0.5414 (tmm) REVERT: B 68 MET cc_start: 0.9208 (mtt) cc_final: 0.8932 (mtt) REVERT: B 100 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8658 (tpm170) REVERT: B 128 GLU cc_start: 0.9396 (mp0) cc_final: 0.9017 (mp0) REVERT: B 129 ILE cc_start: 0.9610 (mm) cc_final: 0.9206 (tp) REVERT: B 190 LEU cc_start: 0.9045 (mt) cc_final: 0.8562 (mt) REVERT: C 53 ASN cc_start: 0.8715 (m-40) cc_final: 0.8363 (t0) REVERT: C 68 MET cc_start: 0.9355 (mtp) cc_final: 0.8740 (mtt) REVERT: C 79 GLU cc_start: 0.9197 (tp30) cc_final: 0.8977 (tp30) REVERT: C 140 LYS cc_start: 0.9417 (mtmm) cc_final: 0.9214 (ptpp) REVERT: C 167 ARG cc_start: 0.9082 (ttt180) cc_final: 0.8745 (ptp-170) REVERT: D 23 TRP cc_start: 0.9617 (t-100) cc_final: 0.9273 (t-100) REVERT: D 55 MET cc_start: 0.9445 (ttm) cc_final: 0.8965 (ttp) REVERT: D 68 MET cc_start: 0.9234 (mtt) cc_final: 0.8637 (mtt) REVERT: D 98 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6421 (mt-10) REVERT: D 129 ILE cc_start: 0.9129 (mt) cc_final: 0.8828 (tt) REVERT: D 132 ARG cc_start: 0.9502 (mtp-110) cc_final: 0.9207 (ttm110) REVERT: D 185 MET cc_start: 0.9567 (ptp) cc_final: 0.9274 (mtt) REVERT: D 212 GLU cc_start: 0.9382 (pt0) cc_final: 0.8790 (pm20) REVERT: D 215 MET cc_start: 0.8800 (mtm) cc_final: 0.8192 (mtm) REVERT: E 10 MET cc_start: 0.5402 (tmm) cc_final: 0.5179 (tmm) REVERT: E 13 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8549 (pp30) REVERT: E 28 GLU cc_start: 0.8765 (tt0) cc_final: 0.8287 (pt0) REVERT: E 30 LYS cc_start: 0.8828 (tppt) cc_final: 0.8234 (tptp) REVERT: E 55 MET cc_start: 0.9662 (ttm) cc_final: 0.9212 (tpp) REVERT: E 66 MET cc_start: 0.9229 (mpp) cc_final: 0.8631 (mpp) REVERT: E 68 MET cc_start: 0.9065 (mtp) cc_final: 0.8838 (mtp) REVERT: E 100 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8714 (tpp-160) REVERT: E 128 GLU cc_start: 0.9220 (mp0) cc_final: 0.8702 (tm-30) REVERT: E 129 ILE cc_start: 0.9491 (mm) cc_final: 0.8518 (mm) REVERT: E 131 LYS cc_start: 0.9656 (tttt) cc_final: 0.9287 (tttt) REVERT: E 132 ARG cc_start: 0.9352 (mtm110) cc_final: 0.8858 (mtm110) REVERT: E 141 ILE cc_start: 0.8973 (mt) cc_final: 0.8531 (mt) REVERT: E 144 MET cc_start: 0.7638 (ppp) cc_final: 0.7388 (ppp) REVERT: F 68 MET cc_start: 0.9419 (mtp) cc_final: 0.8880 (mtt) REVERT: F 70 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9357 (mmmm) REVERT: F 75 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8432 (tm-30) REVERT: F 79 GLU cc_start: 0.9597 (tt0) cc_final: 0.9233 (tp30) REVERT: F 111 LEU cc_start: 0.8783 (tp) cc_final: 0.8556 (mm) REVERT: F 117 TRP cc_start: 0.8376 (m-10) cc_final: 0.7373 (m-90) REVERT: F 129 ILE cc_start: 0.9635 (mt) cc_final: 0.9262 (mm) REVERT: F 132 ARG cc_start: 0.9471 (mtp-110) cc_final: 0.9050 (ptm-80) REVERT: F 141 ILE cc_start: 0.9543 (mt) cc_final: 0.9211 (mt) REVERT: F 143 ARG cc_start: 0.9331 (mtp85) cc_final: 0.9105 (mmm-85) REVERT: F 164 TYR cc_start: 0.8288 (t80) cc_final: 0.6816 (t80) REVERT: F 168 PHE cc_start: 0.9508 (t80) cc_final: 0.8931 (t80) REVERT: F 179 GLN cc_start: 0.9233 (tp-100) cc_final: 0.9002 (tp-100) REVERT: F 185 MET cc_start: 0.8938 (ptp) cc_final: 0.8732 (ptp) REVERT: F 190 LEU cc_start: 0.8984 (mt) cc_final: 0.8357 (mt) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 0.1506 time to fit residues: 87.3870 Evaluate side-chains 369 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 0.0010 chunk 117 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 0.0020 chunk 89 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 139 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN D 95 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN F 155 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.064046 restraints weight = 68132.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067342 restraints weight = 38012.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069749 restraints weight = 25789.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071514 restraints weight = 19383.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072796 restraints weight = 15630.170| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10572 Z= 0.148 Angle : 0.641 9.095 14378 Z= 0.328 Chirality : 0.044 0.180 1604 Planarity : 0.005 0.043 1882 Dihedral : 3.963 21.665 1404 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.22), residues: 1310 helix: 0.51 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.55 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 167 TYR 0.026 0.002 TYR E 130 PHE 0.020 0.002 PHE A 40 TRP 0.043 0.002 TRP D 117 HIS 0.002 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00334 (10566) covalent geometry : angle 0.64122 (14366) SS BOND : bond 0.00065 ( 6) SS BOND : angle 0.79140 ( 12) hydrogen bonds : bond 0.03576 ( 577) hydrogen bonds : angle 3.89449 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PRO cc_start: 0.9272 (Cg_exo) cc_final: 0.9054 (Cg_endo) REVERT: A 68 MET cc_start: 0.9495 (mtp) cc_final: 0.9237 (mtt) REVERT: A 82 ARG cc_start: 0.9368 (ptm-80) cc_final: 0.9163 (ttp80) REVERT: A 100 ARG cc_start: 0.9023 (ptm-80) cc_final: 0.8697 (ptm-80) REVERT: A 129 ILE cc_start: 0.9155 (mt) cc_final: 0.8662 (mt) REVERT: A 141 ILE cc_start: 0.9678 (mm) cc_final: 0.9461 (tp) REVERT: A 144 MET cc_start: 0.8924 (tpp) cc_final: 0.8366 (tpp) REVERT: A 167 ARG cc_start: 0.9227 (mtm-85) cc_final: 0.8710 (ptt-90) REVERT: A 214 MET cc_start: 0.9163 (ptp) cc_final: 0.8904 (ptp) REVERT: A 215 MET cc_start: 0.8489 (ptm) cc_final: 0.7880 (ptm) REVERT: B 10 MET cc_start: 0.6082 (tmm) cc_final: 0.5795 (tmm) REVERT: B 100 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8671 (tpm170) REVERT: B 128 GLU cc_start: 0.9386 (mp0) cc_final: 0.9051 (mp0) REVERT: B 141 ILE cc_start: 0.8971 (mt) cc_final: 0.8767 (mt) REVERT: B 144 MET cc_start: 0.8871 (ppp) cc_final: 0.8321 (ppp) REVERT: B 190 LEU cc_start: 0.9089 (mt) cc_final: 0.8819 (mt) REVERT: C 25 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8566 (tptp) REVERT: C 68 MET cc_start: 0.9264 (mtp) cc_final: 0.8514 (mtm) REVERT: C 164 TYR cc_start: 0.7723 (t80) cc_final: 0.6470 (t80) REVERT: C 167 ARG cc_start: 0.9093 (ttt180) cc_final: 0.8697 (ptp90) REVERT: C 185 MET cc_start: 0.9067 (ptp) cc_final: 0.8613 (ptp) REVERT: D 23 TRP cc_start: 0.9630 (t-100) cc_final: 0.9339 (t-100) REVERT: D 55 MET cc_start: 0.9456 (ttm) cc_final: 0.8939 (ttm) REVERT: D 96 MET cc_start: 0.7201 (tpt) cc_final: 0.6966 (tpp) REVERT: D 111 LEU cc_start: 0.9595 (tp) cc_final: 0.9335 (tp) REVERT: D 128 GLU cc_start: 0.9119 (mp0) cc_final: 0.8815 (mp0) REVERT: D 129 ILE cc_start: 0.9235 (mt) cc_final: 0.8913 (tt) REVERT: D 132 ARG cc_start: 0.9388 (mtp-110) cc_final: 0.9106 (ttm110) REVERT: D 173 ARG cc_start: 0.9511 (ttm-80) cc_final: 0.9231 (ttp80) REVERT: D 185 MET cc_start: 0.9574 (ptp) cc_final: 0.9264 (mtt) REVERT: E 10 MET cc_start: 0.5265 (tmm) cc_final: 0.4908 (tmm) REVERT: E 25 LYS cc_start: 0.9473 (tttp) cc_final: 0.9093 (ttmm) REVERT: E 28 GLU cc_start: 0.8821 (tt0) cc_final: 0.8374 (pt0) REVERT: E 30 LYS cc_start: 0.8881 (tppt) cc_final: 0.8227 (tptp) REVERT: E 55 MET cc_start: 0.9645 (ttm) cc_final: 0.9201 (tpp) REVERT: E 66 MET cc_start: 0.9168 (mpp) cc_final: 0.8491 (mpp) REVERT: E 68 MET cc_start: 0.9152 (mtp) cc_final: 0.8478 (mtp) REVERT: E 72 THR cc_start: 0.8988 (p) cc_final: 0.8362 (p) REVERT: E 100 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8717 (tpp-160) REVERT: E 128 GLU cc_start: 0.9256 (mp0) cc_final: 0.8682 (tm-30) REVERT: E 129 ILE cc_start: 0.9457 (mm) cc_final: 0.8543 (mm) REVERT: E 131 LYS cc_start: 0.9598 (tttt) cc_final: 0.9308 (tttt) REVERT: E 132 ARG cc_start: 0.9358 (mtm110) cc_final: 0.9148 (mtm110) REVERT: E 136 LEU cc_start: 0.9733 (tt) cc_final: 0.9282 (pp) REVERT: E 140 LYS cc_start: 0.9465 (mtpt) cc_final: 0.8998 (mtmm) REVERT: E 141 ILE cc_start: 0.8996 (mt) cc_final: 0.8501 (mt) REVERT: E 179 GLN cc_start: 0.9447 (pm20) cc_final: 0.9048 (pm20) REVERT: F 25 LYS cc_start: 0.8865 (ptmm) cc_final: 0.8642 (ttpp) REVERT: F 33 SER cc_start: 0.9039 (p) cc_final: 0.8769 (p) REVERT: F 39 MET cc_start: 0.9060 (mmt) cc_final: 0.8805 (mmm) REVERT: F 68 MET cc_start: 0.9365 (mtp) cc_final: 0.8814 (mtt) REVERT: F 75 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 79 GLU cc_start: 0.9619 (tt0) cc_final: 0.9295 (tp30) REVERT: F 111 LEU cc_start: 0.8764 (tp) cc_final: 0.8424 (mp) REVERT: F 132 ARG cc_start: 0.9483 (mtp-110) cc_final: 0.9053 (ptm-80) REVERT: F 141 ILE cc_start: 0.9458 (mt) cc_final: 0.9184 (mm) REVERT: F 158 LYS cc_start: 0.8310 (mmpt) cc_final: 0.8046 (tppt) REVERT: F 164 TYR cc_start: 0.7887 (t80) cc_final: 0.6450 (t80) REVERT: F 167 ARG cc_start: 0.9106 (mtm-85) cc_final: 0.8427 (ptp-170) REVERT: F 168 PHE cc_start: 0.9501 (t80) cc_final: 0.8980 (t80) REVERT: F 179 GLN cc_start: 0.9232 (tp-100) cc_final: 0.9015 (tp-100) REVERT: F 185 MET cc_start: 0.9095 (ptp) cc_final: 0.8822 (ptp) REVERT: F 190 LEU cc_start: 0.8983 (mt) cc_final: 0.8613 (mt) outliers start: 1 outliers final: 1 residues processed: 433 average time/residue: 0.1493 time to fit residues: 83.7041 Evaluate side-chains 361 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 4 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.062783 restraints weight = 59773.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065837 restraints weight = 34867.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068018 restraints weight = 24153.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069614 restraints weight = 18389.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070725 restraints weight = 14985.939| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10572 Z= 0.208 Angle : 0.699 7.031 14378 Z= 0.367 Chirality : 0.046 0.174 1604 Planarity : 0.006 0.102 1882 Dihedral : 4.259 22.419 1404 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1310 helix: 0.41 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 173 TYR 0.024 0.002 TYR E 169 PHE 0.022 0.003 PHE E 168 TRP 0.063 0.002 TRP D 117 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00434 (10566) covalent geometry : angle 0.69789 (14366) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.24947 ( 12) hydrogen bonds : bond 0.03792 ( 577) hydrogen bonds : angle 4.18985 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9464 (mtp) cc_final: 0.9036 (mtt) REVERT: A 82 ARG cc_start: 0.9387 (ptm-80) cc_final: 0.9187 (ttp80) REVERT: A 98 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 141 ILE cc_start: 0.9677 (mm) cc_final: 0.9435 (tp) REVERT: A 144 MET cc_start: 0.8880 (tpp) cc_final: 0.8361 (tpp) REVERT: A 163 ASP cc_start: 0.9072 (m-30) cc_final: 0.8764 (m-30) REVERT: A 167 ARG cc_start: 0.9060 (mtm-85) cc_final: 0.8459 (mtt180) REVERT: A 212 GLU cc_start: 0.9578 (pt0) cc_final: 0.9309 (pm20) REVERT: A 214 MET cc_start: 0.9243 (ptp) cc_final: 0.8959 (ptp) REVERT: A 215 MET cc_start: 0.8632 (ptm) cc_final: 0.8058 (ptm) REVERT: B 10 MET cc_start: 0.6322 (tmm) cc_final: 0.5941 (tmm) REVERT: B 66 MET cc_start: 0.9086 (mpp) cc_final: 0.8756 (mpp) REVERT: B 82 ARG cc_start: 0.8529 (tmm160) cc_final: 0.8290 (ttp80) REVERT: B 100 ARG cc_start: 0.8995 (ttp80) cc_final: 0.8643 (tpm170) REVERT: B 128 GLU cc_start: 0.9421 (mp0) cc_final: 0.9131 (mp0) REVERT: B 141 ILE cc_start: 0.9041 (mt) cc_final: 0.8831 (mt) REVERT: B 144 MET cc_start: 0.8871 (ppp) cc_final: 0.8573 (ppp) REVERT: B 190 LEU cc_start: 0.9366 (mt) cc_final: 0.9018 (mt) REVERT: C 32 PHE cc_start: 0.8399 (m-80) cc_final: 0.8148 (m-80) REVERT: C 35 GLU cc_start: 0.9186 (pt0) cc_final: 0.8238 (tm-30) REVERT: C 39 MET cc_start: 0.9012 (tpp) cc_final: 0.8548 (tpp) REVERT: C 68 MET cc_start: 0.9380 (mtp) cc_final: 0.9058 (mtm) REVERT: C 167 ARG cc_start: 0.9166 (ttt180) cc_final: 0.8714 (ptp90) REVERT: C 185 MET cc_start: 0.9110 (ptp) cc_final: 0.8711 (ptp) REVERT: D 28 GLU cc_start: 0.8865 (tt0) cc_final: 0.8569 (pp20) REVERT: D 55 MET cc_start: 0.9452 (ttm) cc_final: 0.9232 (ttp) REVERT: D 96 MET cc_start: 0.7522 (tpt) cc_final: 0.7277 (tpp) REVERT: D 111 LEU cc_start: 0.9583 (tp) cc_final: 0.9325 (tp) REVERT: D 132 ARG cc_start: 0.9416 (mtp-110) cc_final: 0.9138 (ttm110) REVERT: D 173 ARG cc_start: 0.9471 (ttm-80) cc_final: 0.9215 (ttp80) REVERT: E 10 MET cc_start: 0.5512 (tmm) cc_final: 0.5101 (tmm) REVERT: E 25 LYS cc_start: 0.9457 (tttp) cc_final: 0.9099 (ttmm) REVERT: E 28 GLU cc_start: 0.8765 (tt0) cc_final: 0.8247 (pt0) REVERT: E 30 LYS cc_start: 0.8851 (tppt) cc_final: 0.8320 (tptp) REVERT: E 66 MET cc_start: 0.9153 (mpp) cc_final: 0.8581 (mpp) REVERT: E 68 MET cc_start: 0.9182 (mtp) cc_final: 0.8629 (mtp) REVERT: E 100 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8704 (tpp-160) REVERT: E 128 GLU cc_start: 0.9325 (mp0) cc_final: 0.8731 (tm-30) REVERT: E 129 ILE cc_start: 0.9494 (mm) cc_final: 0.8793 (mm) REVERT: E 131 LYS cc_start: 0.9631 (tttt) cc_final: 0.9308 (tttt) REVERT: E 132 ARG cc_start: 0.9413 (mtm110) cc_final: 0.9075 (mtm110) REVERT: E 141 ILE cc_start: 0.9085 (mt) cc_final: 0.8449 (mt) REVERT: E 144 MET cc_start: 0.7784 (ppp) cc_final: 0.7448 (ppp) REVERT: F 25 LYS cc_start: 0.8874 (ptmm) cc_final: 0.8605 (ttpp) REVERT: F 55 MET cc_start: 0.8931 (ttp) cc_final: 0.8552 (tmm) REVERT: F 68 MET cc_start: 0.9377 (mtp) cc_final: 0.8840 (mtt) REVERT: F 79 GLU cc_start: 0.9606 (tt0) cc_final: 0.9282 (tp30) REVERT: F 128 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8763 (tm-30) REVERT: F 129 ILE cc_start: 0.9630 (pt) cc_final: 0.9339 (pt) REVERT: F 132 ARG cc_start: 0.9495 (mtp-110) cc_final: 0.9037 (ptm-80) REVERT: F 141 ILE cc_start: 0.9481 (mt) cc_final: 0.9199 (mm) REVERT: F 143 ARG cc_start: 0.9256 (mmm-85) cc_final: 0.9050 (mmm-85) REVERT: F 158 LYS cc_start: 0.8224 (mmpt) cc_final: 0.8004 (tppt) REVERT: F 164 TYR cc_start: 0.8050 (t80) cc_final: 0.6544 (t80) REVERT: F 167 ARG cc_start: 0.9161 (mtm-85) cc_final: 0.8688 (mtm-85) REVERT: F 168 PHE cc_start: 0.9568 (t80) cc_final: 0.9148 (t80) REVERT: F 179 GLN cc_start: 0.9284 (tp-100) cc_final: 0.9025 (tp-100) REVERT: F 185 MET cc_start: 0.9121 (ptp) cc_final: 0.8856 (ptp) REVERT: F 190 LEU cc_start: 0.8970 (mt) cc_final: 0.8565 (mt) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.1482 time to fit residues: 79.7117 Evaluate side-chains 339 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.061973 restraints weight = 92017.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065656 restraints weight = 44450.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068310 restraints weight = 28353.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070285 restraints weight = 20461.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071716 restraints weight = 16014.732| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10572 Z= 0.157 Angle : 0.688 7.958 14378 Z= 0.355 Chirality : 0.045 0.200 1604 Planarity : 0.006 0.122 1882 Dihedral : 4.327 21.094 1404 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.23), residues: 1310 helix: 0.56 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.63 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 143 TYR 0.032 0.002 TYR B 169 PHE 0.019 0.002 PHE A 40 TRP 0.057 0.002 TRP D 117 HIS 0.003 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00351 (10566) covalent geometry : angle 0.68683 (14366) SS BOND : bond 0.00334 ( 6) SS BOND : angle 1.37040 ( 12) hydrogen bonds : bond 0.03786 ( 577) hydrogen bonds : angle 4.14572 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9459 (mtp) cc_final: 0.9204 (mtt) REVERT: A 98 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 100 ARG cc_start: 0.8978 (ptm-80) cc_final: 0.8725 (ptm-80) REVERT: A 129 ILE cc_start: 0.9071 (mt) cc_final: 0.8732 (mt) REVERT: A 144 MET cc_start: 0.9022 (tpp) cc_final: 0.8554 (tpp) REVERT: A 167 ARG cc_start: 0.9057 (mtm-85) cc_final: 0.8651 (mtm180) REVERT: A 212 GLU cc_start: 0.9450 (pt0) cc_final: 0.9128 (pm20) REVERT: A 214 MET cc_start: 0.9247 (ptp) cc_final: 0.8967 (ptp) REVERT: A 215 MET cc_start: 0.8731 (ptm) cc_final: 0.8069 (ptm) REVERT: B 10 MET cc_start: 0.6430 (tmm) cc_final: 0.5866 (tmm) REVERT: B 55 MET cc_start: 0.9586 (ttm) cc_final: 0.9218 (ttm) REVERT: B 68 MET cc_start: 0.8964 (mtt) cc_final: 0.8332 (mtp) REVERT: B 71 GLU cc_start: 0.8992 (pp20) cc_final: 0.8711 (pp20) REVERT: B 72 THR cc_start: 0.9065 (p) cc_final: 0.8505 (p) REVERT: B 82 ARG cc_start: 0.8504 (tmm160) cc_final: 0.8074 (ttp80) REVERT: B 100 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8605 (tpm170) REVERT: B 128 GLU cc_start: 0.9425 (mp0) cc_final: 0.9122 (mp0) REVERT: B 141 ILE cc_start: 0.9050 (mt) cc_final: 0.8781 (mt) REVERT: B 144 MET cc_start: 0.8909 (ppp) cc_final: 0.8447 (ppp) REVERT: C 68 MET cc_start: 0.9445 (mtp) cc_final: 0.8760 (mtt) REVERT: C 154 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8226 (mmm-85) REVERT: C 167 ARG cc_start: 0.9215 (ttt180) cc_final: 0.8794 (ptp90) REVERT: C 185 MET cc_start: 0.9110 (ptp) cc_final: 0.8746 (ptp) REVERT: C 215 MET cc_start: 0.9009 (ppp) cc_final: 0.8763 (ppp) REVERT: C 216 THR cc_start: 0.8567 (p) cc_final: 0.8304 (p) REVERT: D 23 TRP cc_start: 0.9640 (t-100) cc_final: 0.9193 (t-100) REVERT: D 28 GLU cc_start: 0.8909 (tt0) cc_final: 0.8547 (pp20) REVERT: D 40 PHE cc_start: 0.9608 (t80) cc_final: 0.9399 (t80) REVERT: D 55 MET cc_start: 0.9427 (ttm) cc_final: 0.8949 (ttp) REVERT: D 70 LYS cc_start: 0.9521 (mtpt) cc_final: 0.9198 (ptpt) REVERT: D 96 MET cc_start: 0.7415 (tpt) cc_final: 0.7201 (tpp) REVERT: D 111 LEU cc_start: 0.9615 (tp) cc_final: 0.9367 (tp) REVERT: D 128 GLU cc_start: 0.8935 (pm20) cc_final: 0.8666 (tm-30) REVERT: D 173 ARG cc_start: 0.9435 (ttm-80) cc_final: 0.9223 (ttp80) REVERT: D 185 MET cc_start: 0.9587 (ptp) cc_final: 0.9217 (mtt) REVERT: D 214 MET cc_start: 0.9123 (ptp) cc_final: 0.8888 (ptp) REVERT: D 215 MET cc_start: 0.8959 (ptm) cc_final: 0.8600 (ptt) REVERT: E 10 MET cc_start: 0.5590 (tmm) cc_final: 0.4827 (tmm) REVERT: E 25 LYS cc_start: 0.9408 (tttp) cc_final: 0.9183 (ttmm) REVERT: E 28 GLU cc_start: 0.8723 (tt0) cc_final: 0.8242 (pt0) REVERT: E 30 LYS cc_start: 0.8874 (tppt) cc_final: 0.8430 (tptp) REVERT: E 66 MET cc_start: 0.9181 (mpp) cc_final: 0.8674 (mpp) REVERT: E 68 MET cc_start: 0.9214 (mtp) cc_final: 0.8619 (mtp) REVERT: E 72 THR cc_start: 0.9020 (p) cc_final: 0.8517 (p) REVERT: E 100 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8707 (tpp-160) REVERT: E 128 GLU cc_start: 0.9363 (mp0) cc_final: 0.8700 (tm-30) REVERT: E 129 ILE cc_start: 0.9475 (mm) cc_final: 0.8955 (mm) REVERT: E 132 ARG cc_start: 0.9433 (mtm110) cc_final: 0.9116 (mtm110) REVERT: E 141 ILE cc_start: 0.9089 (mt) cc_final: 0.8487 (mt) REVERT: E 144 MET cc_start: 0.7742 (ppp) cc_final: 0.7434 (ppp) REVERT: E 215 MET cc_start: 0.8707 (mmp) cc_final: 0.8296 (mmp) REVERT: F 68 MET cc_start: 0.9446 (mtp) cc_final: 0.8761 (mtt) REVERT: F 71 GLU cc_start: 0.8735 (pp20) cc_final: 0.8352 (pp20) REVERT: F 79 GLU cc_start: 0.9607 (tt0) cc_final: 0.9313 (tp30) REVERT: F 81 ASP cc_start: 0.9053 (m-30) cc_final: 0.8840 (m-30) REVERT: F 103 ASP cc_start: 0.9096 (m-30) cc_final: 0.8743 (m-30) REVERT: F 128 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8769 (tm-30) REVERT: F 129 ILE cc_start: 0.9606 (pt) cc_final: 0.9269 (pt) REVERT: F 132 ARG cc_start: 0.9501 (mtp-110) cc_final: 0.9033 (ptm-80) REVERT: F 143 ARG cc_start: 0.9197 (mmm-85) cc_final: 0.8847 (mmm-85) REVERT: F 158 LYS cc_start: 0.8310 (mmpt) cc_final: 0.7938 (tppt) REVERT: F 164 TYR cc_start: 0.8230 (t80) cc_final: 0.7727 (t80) REVERT: F 167 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8449 (ptp-170) REVERT: F 179 GLN cc_start: 0.9303 (tp-100) cc_final: 0.9050 (tp-100) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1442 time to fit residues: 78.1073 Evaluate side-chains 335 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 79 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.062499 restraints weight = 69092.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065721 restraints weight = 38226.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068126 restraints weight = 25805.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069879 restraints weight = 19273.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071189 restraints weight = 15469.066| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10572 Z= 0.158 Angle : 0.698 8.145 14378 Z= 0.359 Chirality : 0.046 0.176 1604 Planarity : 0.005 0.062 1882 Dihedral : 4.345 19.922 1404 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.23), residues: 1310 helix: 0.61 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.61 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 82 TYR 0.024 0.002 TYR B 169 PHE 0.020 0.003 PHE B 40 TRP 0.048 0.002 TRP D 117 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00361 (10566) covalent geometry : angle 0.69788 (14366) SS BOND : bond 0.00130 ( 6) SS BOND : angle 1.16145 ( 12) hydrogen bonds : bond 0.03698 ( 577) hydrogen bonds : angle 4.14883 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9354 (ttm) cc_final: 0.9136 (ttp) REVERT: A 68 MET cc_start: 0.9404 (mtp) cc_final: 0.9093 (mtt) REVERT: A 70 LYS cc_start: 0.9462 (ttmm) cc_final: 0.9259 (ptpp) REVERT: A 96 MET cc_start: 0.6133 (tpt) cc_final: 0.5687 (tpp) REVERT: A 98 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 129 ILE cc_start: 0.9059 (mt) cc_final: 0.8653 (mt) REVERT: A 144 MET cc_start: 0.8987 (tpp) cc_final: 0.8477 (tpp) REVERT: A 167 ARG cc_start: 0.9043 (mtm-85) cc_final: 0.8653 (mtm180) REVERT: A 214 MET cc_start: 0.9253 (ptp) cc_final: 0.8977 (ptp) REVERT: A 215 MET cc_start: 0.8575 (ptm) cc_final: 0.8153 (ptm) REVERT: B 10 MET cc_start: 0.6336 (tmm) cc_final: 0.5769 (tmm) REVERT: B 55 MET cc_start: 0.9642 (ttm) cc_final: 0.9354 (ttm) REVERT: B 72 THR cc_start: 0.9041 (p) cc_final: 0.8799 (p) REVERT: B 100 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8549 (mmp80) REVERT: B 128 GLU cc_start: 0.9437 (mp0) cc_final: 0.9127 (mp0) REVERT: C 32 PHE cc_start: 0.8454 (m-80) cc_final: 0.8144 (m-80) REVERT: C 68 MET cc_start: 0.9350 (mtp) cc_final: 0.9015 (mtt) REVERT: C 114 GLN cc_start: 0.8891 (mt0) cc_final: 0.8646 (mt0) REVERT: C 154 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8292 (mmm-85) REVERT: C 167 ARG cc_start: 0.9236 (ttt180) cc_final: 0.8838 (ptp90) REVERT: C 169 TYR cc_start: 0.8810 (m-80) cc_final: 0.8610 (m-80) REVERT: C 185 MET cc_start: 0.9086 (ptp) cc_final: 0.8700 (ptp) REVERT: C 215 MET cc_start: 0.9032 (ppp) cc_final: 0.8791 (ppp) REVERT: C 216 THR cc_start: 0.8732 (p) cc_final: 0.8431 (p) REVERT: D 55 MET cc_start: 0.9419 (ttm) cc_final: 0.9209 (ttp) REVERT: D 70 LYS cc_start: 0.9496 (mtpt) cc_final: 0.9195 (ptpt) REVERT: D 71 GLU cc_start: 0.9049 (pp20) cc_final: 0.8661 (pp20) REVERT: D 96 MET cc_start: 0.7570 (tpt) cc_final: 0.7331 (tpp) REVERT: D 111 LEU cc_start: 0.9615 (tp) cc_final: 0.9382 (tp) REVERT: D 128 GLU cc_start: 0.8896 (pm20) cc_final: 0.8483 (tm-30) REVERT: D 185 MET cc_start: 0.9566 (ptp) cc_final: 0.9171 (mtt) REVERT: D 211 LEU cc_start: 0.9729 (tp) cc_final: 0.9510 (tp) REVERT: D 215 MET cc_start: 0.8888 (ptm) cc_final: 0.8472 (ptm) REVERT: E 10 MET cc_start: 0.5831 (tmm) cc_final: 0.5150 (tmm) REVERT: E 25 LYS cc_start: 0.9430 (tttp) cc_final: 0.9083 (ttmm) REVERT: E 28 GLU cc_start: 0.8701 (tt0) cc_final: 0.8153 (pt0) REVERT: E 30 LYS cc_start: 0.8848 (tppt) cc_final: 0.8405 (tptp) REVERT: E 66 MET cc_start: 0.9182 (mpp) cc_final: 0.8608 (mpp) REVERT: E 68 MET cc_start: 0.9184 (mtp) cc_final: 0.8614 (mtp) REVERT: E 72 THR cc_start: 0.9026 (p) cc_final: 0.8519 (p) REVERT: E 100 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8689 (tpp-160) REVERT: E 128 GLU cc_start: 0.9341 (mp0) cc_final: 0.8735 (tm-30) REVERT: E 129 ILE cc_start: 0.9471 (mm) cc_final: 0.8640 (mm) REVERT: E 132 ARG cc_start: 0.9450 (mtm110) cc_final: 0.9049 (mtm110) REVERT: E 141 ILE cc_start: 0.9115 (mt) cc_final: 0.8770 (mt) REVERT: F 68 MET cc_start: 0.9227 (mtp) cc_final: 0.8830 (mtp) REVERT: F 79 GLU cc_start: 0.9608 (tt0) cc_final: 0.9325 (tp30) REVERT: F 81 ASP cc_start: 0.9142 (m-30) cc_final: 0.8818 (m-30) REVERT: F 100 ARG cc_start: 0.8094 (mmp80) cc_final: 0.7852 (mmp-170) REVERT: F 103 ASP cc_start: 0.9101 (m-30) cc_final: 0.8763 (m-30) REVERT: F 141 ILE cc_start: 0.9382 (mm) cc_final: 0.9073 (mt) REVERT: F 158 LYS cc_start: 0.8283 (mmpt) cc_final: 0.8044 (tppt) REVERT: F 164 TYR cc_start: 0.8328 (t80) cc_final: 0.7091 (t80) REVERT: F 167 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8400 (mtt180) REVERT: F 173 ARG cc_start: 0.9348 (tmm-80) cc_final: 0.8921 (tmt170) REVERT: F 179 GLN cc_start: 0.9254 (tp-100) cc_final: 0.8969 (tp-100) REVERT: F 185 MET cc_start: 0.9078 (ptp) cc_final: 0.8808 (ptp) outliers start: 1 outliers final: 1 residues processed: 401 average time/residue: 0.1383 time to fit residues: 72.7847 Evaluate side-chains 318 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060149 restraints weight = 89438.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.063684 restraints weight = 44834.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066256 restraints weight = 28897.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068172 restraints weight = 21109.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.069581 restraints weight = 16571.759| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10572 Z= 0.187 Angle : 0.725 7.581 14378 Z= 0.380 Chirality : 0.047 0.186 1604 Planarity : 0.005 0.065 1882 Dihedral : 4.480 23.285 1404 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1310 helix: 0.53 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.73 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 82 TYR 0.026 0.002 TYR E 130 PHE 0.027 0.003 PHE B 168 TRP 0.043 0.002 TRP D 117 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00414 (10566) covalent geometry : angle 0.72419 (14366) SS BOND : bond 0.00294 ( 6) SS BOND : angle 1.51450 ( 12) hydrogen bonds : bond 0.03876 ( 577) hydrogen bonds : angle 4.33341 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9383 (mtp) cc_final: 0.9140 (mtt) REVERT: A 71 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9197 (tm-30) REVERT: A 98 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 144 MET cc_start: 0.9037 (tpp) cc_final: 0.8551 (tpp) REVERT: A 214 MET cc_start: 0.9341 (ptp) cc_final: 0.9049 (ptp) REVERT: A 215 MET cc_start: 0.8632 (ptm) cc_final: 0.8224 (ptm) REVERT: B 10 MET cc_start: 0.6314 (tmm) cc_final: 0.5986 (tmm) REVERT: B 55 MET cc_start: 0.9597 (ttm) cc_final: 0.9167 (ttm) REVERT: B 128 GLU cc_start: 0.9489 (mp0) cc_final: 0.9157 (mp0) REVERT: B 141 ILE cc_start: 0.9101 (mt) cc_final: 0.8887 (mt) REVERT: B 144 MET cc_start: 0.8643 (ppp) cc_final: 0.8442 (ppp) REVERT: C 32 PHE cc_start: 0.8481 (m-80) cc_final: 0.8215 (m-80) REVERT: C 68 MET cc_start: 0.9267 (mtp) cc_final: 0.8924 (mtt) REVERT: C 81 ASP cc_start: 0.9162 (m-30) cc_final: 0.8837 (m-30) REVERT: C 103 ASP cc_start: 0.9047 (m-30) cc_final: 0.8789 (m-30) REVERT: C 129 ILE cc_start: 0.9671 (pt) cc_final: 0.9433 (pt) REVERT: C 131 LYS cc_start: 0.9345 (ptpp) cc_final: 0.9124 (pttm) REVERT: C 154 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8301 (mmm-85) REVERT: C 167 ARG cc_start: 0.9299 (ttt180) cc_final: 0.8874 (ptp-170) REVERT: C 185 MET cc_start: 0.9153 (ptp) cc_final: 0.8820 (ptp) REVERT: C 215 MET cc_start: 0.9048 (ppp) cc_final: 0.8812 (ppp) REVERT: C 216 THR cc_start: 0.8440 (p) cc_final: 0.8187 (p) REVERT: D 28 GLU cc_start: 0.8894 (tt0) cc_final: 0.8581 (pp20) REVERT: D 55 MET cc_start: 0.9416 (ttm) cc_final: 0.9209 (ttp) REVERT: D 70 LYS cc_start: 0.9493 (mtpt) cc_final: 0.9201 (ptpt) REVERT: D 71 GLU cc_start: 0.9085 (pp20) cc_final: 0.8687 (pp20) REVERT: D 96 MET cc_start: 0.7633 (tpt) cc_final: 0.7279 (tpp) REVERT: D 111 LEU cc_start: 0.9602 (tp) cc_final: 0.9368 (tp) REVERT: D 115 ILE cc_start: 0.9510 (mm) cc_final: 0.9239 (mm) REVERT: D 128 GLU cc_start: 0.8706 (pm20) cc_final: 0.8365 (tm-30) REVERT: D 185 MET cc_start: 0.9562 (ptp) cc_final: 0.9176 (mtt) REVERT: D 214 MET cc_start: 0.9215 (ptp) cc_final: 0.8963 (ptp) REVERT: E 10 MET cc_start: 0.5581 (tmm) cc_final: 0.5136 (tmm) REVERT: E 25 LYS cc_start: 0.9435 (tttp) cc_final: 0.9167 (ttmm) REVERT: E 28 GLU cc_start: 0.8688 (tt0) cc_final: 0.8215 (pt0) REVERT: E 30 LYS cc_start: 0.8858 (tppt) cc_final: 0.8425 (tptp) REVERT: E 55 MET cc_start: 0.9629 (ttm) cc_final: 0.9203 (ttm) REVERT: E 66 MET cc_start: 0.9185 (mpp) cc_final: 0.8555 (mpp) REVERT: E 68 MET cc_start: 0.9222 (mtp) cc_final: 0.8750 (mtp) REVERT: E 100 ARG cc_start: 0.9166 (ttp80) cc_final: 0.8713 (tpp-160) REVERT: E 128 GLU cc_start: 0.9358 (mp0) cc_final: 0.8739 (tm-30) REVERT: E 129 ILE cc_start: 0.9471 (mm) cc_final: 0.8657 (mm) REVERT: E 131 LYS cc_start: 0.9683 (tttt) cc_final: 0.9463 (tptt) REVERT: E 132 ARG cc_start: 0.9481 (mtm110) cc_final: 0.9113 (mtm110) REVERT: E 141 ILE cc_start: 0.9124 (mt) cc_final: 0.8486 (mt) REVERT: E 144 MET cc_start: 0.7698 (ppp) cc_final: 0.7417 (ppp) REVERT: E 173 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.9129 (mmm160) REVERT: F 9 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8401 (pp30) REVERT: F 79 GLU cc_start: 0.9607 (tt0) cc_final: 0.9319 (tp30) REVERT: F 81 ASP cc_start: 0.9143 (m-30) cc_final: 0.8859 (m-30) REVERT: F 100 ARG cc_start: 0.8125 (mmp80) cc_final: 0.7790 (mmp-170) REVERT: F 103 ASP cc_start: 0.9068 (m-30) cc_final: 0.8707 (m-30) REVERT: F 132 ARG cc_start: 0.9614 (mtm110) cc_final: 0.9172 (ptm-80) REVERT: F 158 LYS cc_start: 0.8368 (mmpt) cc_final: 0.8119 (tppt) REVERT: F 164 TYR cc_start: 0.8224 (t80) cc_final: 0.7782 (t80) REVERT: F 167 ARG cc_start: 0.9082 (mtm-85) cc_final: 0.8527 (mtt180) REVERT: F 179 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8975 (tp-100) REVERT: F 182 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8123 (ptpt) REVERT: F 185 MET cc_start: 0.9109 (ptp) cc_final: 0.8898 (ptp) REVERT: F 215 MET cc_start: 0.9335 (ppp) cc_final: 0.9128 (ppp) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1331 time to fit residues: 68.0809 Evaluate side-chains 308 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 91 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 0.0370 chunk 123 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062815 restraints weight = 57040.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065758 restraints weight = 34206.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067920 restraints weight = 24028.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069491 restraints weight = 18444.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070668 restraints weight = 15081.935| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10572 Z= 0.153 Angle : 0.730 7.667 14378 Z= 0.378 Chirality : 0.047 0.171 1604 Planarity : 0.005 0.041 1882 Dihedral : 4.418 22.714 1404 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1310 helix: 0.59 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.72 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 82 TYR 0.017 0.002 TYR B 169 PHE 0.022 0.003 PHE B 40 TRP 0.053 0.002 TRP D 117 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00353 (10566) covalent geometry : angle 0.72861 (14366) SS BOND : bond 0.00143 ( 6) SS BOND : angle 1.50094 ( 12) hydrogen bonds : bond 0.03797 ( 577) hydrogen bonds : angle 4.39933 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9157 (mm-30) cc_final: 0.7862 (pp20) REVERT: A 29 GLU cc_start: 0.8013 (pt0) cc_final: 0.7364 (pt0) REVERT: A 45 GLU cc_start: 0.9312 (tt0) cc_final: 0.8994 (mm-30) REVERT: A 68 MET cc_start: 0.9455 (mtp) cc_final: 0.9138 (mtt) REVERT: A 98 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 109 SER cc_start: 0.8398 (m) cc_final: 0.8151 (m) REVERT: A 176 GLN cc_start: 0.8808 (pm20) cc_final: 0.7639 (pp30) REVERT: A 214 MET cc_start: 0.9294 (ptp) cc_final: 0.9021 (ptp) REVERT: A 215 MET cc_start: 0.8779 (ptm) cc_final: 0.8178 (ptm) REVERT: B 10 MET cc_start: 0.6385 (tmm) cc_final: 0.6119 (tmm) REVERT: B 55 MET cc_start: 0.9578 (ttm) cc_final: 0.9195 (ttm) REVERT: B 68 MET cc_start: 0.8900 (mtp) cc_final: 0.8161 (mtp) REVERT: B 72 THR cc_start: 0.9181 (p) cc_final: 0.8265 (p) REVERT: B 128 GLU cc_start: 0.9395 (mp0) cc_final: 0.9071 (mp0) REVERT: C 32 PHE cc_start: 0.8354 (m-80) cc_final: 0.8135 (m-80) REVERT: C 68 MET cc_start: 0.9382 (mtp) cc_final: 0.9066 (mtt) REVERT: C 81 ASP cc_start: 0.9192 (m-30) cc_final: 0.8979 (m-30) REVERT: C 129 ILE cc_start: 0.9647 (pt) cc_final: 0.9391 (pt) REVERT: C 154 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8314 (mmm-85) REVERT: C 167 ARG cc_start: 0.9269 (ttt180) cc_final: 0.8824 (ptp90) REVERT: C 185 MET cc_start: 0.9104 (ptp) cc_final: 0.8792 (ptp) REVERT: C 215 MET cc_start: 0.9090 (ppp) cc_final: 0.8835 (ppp) REVERT: C 216 THR cc_start: 0.8491 (p) cc_final: 0.8248 (p) REVERT: D 40 PHE cc_start: 0.9466 (t80) cc_final: 0.9235 (t80) REVERT: D 55 MET cc_start: 0.9427 (ttm) cc_final: 0.9175 (ttp) REVERT: D 70 LYS cc_start: 0.9488 (mtpt) cc_final: 0.9254 (ptpt) REVERT: D 71 GLU cc_start: 0.9037 (pp20) cc_final: 0.8644 (pp20) REVERT: D 98 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6674 (tt0) REVERT: D 128 GLU cc_start: 0.8751 (pm20) cc_final: 0.8263 (tm-30) REVERT: D 185 MET cc_start: 0.9557 (ptp) cc_final: 0.9171 (mtt) REVERT: D 214 MET cc_start: 0.9205 (ptp) cc_final: 0.8970 (ptp) REVERT: E 10 MET cc_start: 0.5918 (tmm) cc_final: 0.5467 (tmm) REVERT: E 25 LYS cc_start: 0.9419 (tttp) cc_final: 0.9074 (ttmm) REVERT: E 28 GLU cc_start: 0.8692 (tt0) cc_final: 0.8125 (pt0) REVERT: E 30 LYS cc_start: 0.8792 (tppt) cc_final: 0.8353 (tptp) REVERT: E 66 MET cc_start: 0.9201 (mpp) cc_final: 0.8537 (mpp) REVERT: E 68 MET cc_start: 0.9201 (mtp) cc_final: 0.8738 (mtp) REVERT: E 72 THR cc_start: 0.9053 (p) cc_final: 0.8777 (p) REVERT: E 100 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8728 (tpp-160) REVERT: E 128 GLU cc_start: 0.9377 (mp0) cc_final: 0.8929 (pp20) REVERT: E 131 LYS cc_start: 0.9672 (tttt) cc_final: 0.9449 (tptt) REVERT: E 132 ARG cc_start: 0.9443 (mtm110) cc_final: 0.9011 (mtm110) REVERT: E 141 ILE cc_start: 0.9109 (mt) cc_final: 0.8438 (mt) REVERT: E 144 MET cc_start: 0.7625 (ppp) cc_final: 0.7321 (ppp) REVERT: E 173 ARG cc_start: 0.9348 (mmm-85) cc_final: 0.9120 (mmm160) REVERT: E 211 LEU cc_start: 0.9604 (pt) cc_final: 0.9388 (pt) REVERT: F 9 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8394 (pp30) REVERT: F 10 MET cc_start: 0.8317 (ppp) cc_final: 0.7670 (tmm) REVERT: F 79 GLU cc_start: 0.9605 (tt0) cc_final: 0.9334 (tp30) REVERT: F 81 ASP cc_start: 0.9067 (m-30) cc_final: 0.8828 (m-30) REVERT: F 103 ASP cc_start: 0.9020 (m-30) cc_final: 0.8799 (m-30) REVERT: F 132 ARG cc_start: 0.9610 (mtm110) cc_final: 0.9381 (mtm110) REVERT: F 158 LYS cc_start: 0.8345 (mmpt) cc_final: 0.7986 (tppt) REVERT: F 164 TYR cc_start: 0.8261 (t80) cc_final: 0.7806 (t80) REVERT: F 167 ARG cc_start: 0.9069 (mtm-85) cc_final: 0.8510 (mtt180) REVERT: F 179 GLN cc_start: 0.9285 (tp-100) cc_final: 0.9005 (tp-100) REVERT: F 182 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8178 (ptpt) REVERT: F 185 MET cc_start: 0.9085 (ptp) cc_final: 0.8878 (ptp) REVERT: F 215 MET cc_start: 0.9345 (ppp) cc_final: 0.9101 (ppp) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1301 time to fit residues: 68.7229 Evaluate side-chains 320 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 102 optimal weight: 0.0970 chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061678 restraints weight = 76189.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065118 restraints weight = 40331.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067598 restraints weight = 26727.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.069417 restraints weight = 19792.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070736 restraints weight = 15790.123| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.7383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10572 Z= 0.144 Angle : 0.741 7.889 14378 Z= 0.383 Chirality : 0.048 0.167 1604 Planarity : 0.005 0.048 1882 Dihedral : 4.407 25.214 1404 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1310 helix: 0.56 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.67 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 82 TYR 0.026 0.002 TYR E 130 PHE 0.020 0.003 PHE A 40 TRP 0.050 0.002 TRP D 117 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00338 (10566) covalent geometry : angle 0.73972 (14366) SS BOND : bond 0.00177 ( 6) SS BOND : angle 1.48666 ( 12) hydrogen bonds : bond 0.03934 ( 577) hydrogen bonds : angle 4.36279 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5679 (tpt) cc_final: 0.5346 (mmm) REVERT: A 28 GLU cc_start: 0.9147 (mm-30) cc_final: 0.7856 (pp20) REVERT: A 29 GLU cc_start: 0.7984 (pt0) cc_final: 0.7375 (pt0) REVERT: A 45 GLU cc_start: 0.9261 (tt0) cc_final: 0.8765 (pm20) REVERT: A 68 MET cc_start: 0.9439 (mtp) cc_final: 0.9217 (mtt) REVERT: A 109 SER cc_start: 0.8402 (m) cc_final: 0.8186 (m) REVERT: A 214 MET cc_start: 0.9287 (ptp) cc_final: 0.9021 (ptp) REVERT: A 215 MET cc_start: 0.8777 (ptm) cc_final: 0.8205 (ptm) REVERT: B 10 MET cc_start: 0.6395 (tmm) cc_final: 0.5787 (tmm) REVERT: B 68 MET cc_start: 0.8728 (mtp) cc_final: 0.8368 (mtp) REVERT: B 71 GLU cc_start: 0.8829 (pp20) cc_final: 0.8551 (pp20) REVERT: B 72 THR cc_start: 0.8930 (p) cc_final: 0.8359 (p) REVERT: B 128 GLU cc_start: 0.9406 (mp0) cc_final: 0.9079 (mp0) REVERT: B 144 MET cc_start: 0.8603 (ppp) cc_final: 0.8387 (ppp) REVERT: C 32 PHE cc_start: 0.8378 (m-80) cc_final: 0.8149 (m-80) REVERT: C 68 MET cc_start: 0.9336 (mtp) cc_final: 0.9033 (mtt) REVERT: C 81 ASP cc_start: 0.9183 (m-30) cc_final: 0.8900 (m-30) REVERT: C 154 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8085 (tpp80) REVERT: C 167 ARG cc_start: 0.9257 (ttt180) cc_final: 0.8831 (ptp90) REVERT: C 185 MET cc_start: 0.9092 (ptp) cc_final: 0.8767 (ptp) REVERT: C 215 MET cc_start: 0.9086 (ppp) cc_final: 0.8845 (ppp) REVERT: C 216 THR cc_start: 0.8417 (p) cc_final: 0.8117 (p) REVERT: D 40 PHE cc_start: 0.9425 (t80) cc_final: 0.9212 (t80) REVERT: D 55 MET cc_start: 0.9438 (ttm) cc_final: 0.9236 (ttp) REVERT: D 70 LYS cc_start: 0.9479 (mtpt) cc_final: 0.9239 (ptpt) REVERT: D 71 GLU cc_start: 0.8999 (pp20) cc_final: 0.8635 (pp20) REVERT: D 98 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6773 (tt0) REVERT: D 111 LEU cc_start: 0.9585 (tp) cc_final: 0.9313 (tp) REVERT: D 115 ILE cc_start: 0.9521 (mm) cc_final: 0.9263 (mm) REVERT: D 128 GLU cc_start: 0.8740 (pm20) cc_final: 0.8206 (tm-30) REVERT: D 185 MET cc_start: 0.9545 (ptp) cc_final: 0.9174 (mtt) REVERT: E 10 MET cc_start: 0.5659 (tmm) cc_final: 0.5011 (tmm) REVERT: E 25 LYS cc_start: 0.9394 (tttp) cc_final: 0.9050 (ttmm) REVERT: E 28 GLU cc_start: 0.8686 (tt0) cc_final: 0.8108 (pt0) REVERT: E 30 LYS cc_start: 0.8780 (tppt) cc_final: 0.8346 (tptp) REVERT: E 68 MET cc_start: 0.9164 (mtp) cc_final: 0.8807 (mtp) REVERT: E 72 THR cc_start: 0.9182 (p) cc_final: 0.8800 (p) REVERT: E 100 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8730 (tpp-160) REVERT: E 128 GLU cc_start: 0.9380 (mp0) cc_final: 0.8916 (pp20) REVERT: E 131 LYS cc_start: 0.9664 (tttt) cc_final: 0.9441 (tptt) REVERT: E 132 ARG cc_start: 0.9435 (mtm110) cc_final: 0.8994 (mtm110) REVERT: E 141 ILE cc_start: 0.9058 (mt) cc_final: 0.8450 (mt) REVERT: E 144 MET cc_start: 0.7571 (ppp) cc_final: 0.7229 (ppp) REVERT: E 173 ARG cc_start: 0.9386 (mmm-85) cc_final: 0.9149 (mmm160) REVERT: F 9 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8420 (pp30) REVERT: F 10 MET cc_start: 0.8315 (ppp) cc_final: 0.7712 (tmm) REVERT: F 53 ASN cc_start: 0.8759 (t0) cc_final: 0.8520 (t0) REVERT: F 55 MET cc_start: 0.8759 (tmm) cc_final: 0.8530 (tmm) REVERT: F 79 GLU cc_start: 0.9598 (tt0) cc_final: 0.9356 (tp30) REVERT: F 81 ASP cc_start: 0.8987 (m-30) cc_final: 0.8770 (m-30) REVERT: F 103 ASP cc_start: 0.9004 (m-30) cc_final: 0.8776 (m-30) REVERT: F 132 ARG cc_start: 0.9664 (mtm110) cc_final: 0.9194 (ptm-80) REVERT: F 158 LYS cc_start: 0.8340 (mmpt) cc_final: 0.7949 (tppt) REVERT: F 164 TYR cc_start: 0.8256 (t80) cc_final: 0.7890 (t80) REVERT: F 167 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.8499 (mtt180) REVERT: F 173 ARG cc_start: 0.9388 (tmm-80) cc_final: 0.8953 (tmt170) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1326 time to fit residues: 67.9657 Evaluate side-chains 327 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 192 GLN ** F 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061133 restraints weight = 88479.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.064748 restraints weight = 43828.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067282 restraints weight = 28021.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069198 restraints weight = 20493.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070620 restraints weight = 16025.237| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10572 Z= 0.145 Angle : 0.738 7.747 14378 Z= 0.379 Chirality : 0.047 0.169 1604 Planarity : 0.005 0.040 1882 Dihedral : 4.342 25.308 1404 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1310 helix: 0.58 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.65 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 82 TYR 0.014 0.002 TYR B 169 PHE 0.031 0.003 PHE F 168 TRP 0.045 0.002 TRP D 117 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00337 (10566) covalent geometry : angle 0.73726 (14366) SS BOND : bond 0.00150 ( 6) SS BOND : angle 1.33856 ( 12) hydrogen bonds : bond 0.03771 ( 577) hydrogen bonds : angle 4.33981 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.48 seconds wall clock time: 39 minutes 57.27 seconds (2397.27 seconds total)